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This further validates the biological meanings of the weights extracted from the general properties of the PPI complex network conformation.
In the Network conformation, the PHC is formally situated in the center, being an articulator between the other levels of the system.
Molecular elements like motors and transient cross-linkers directly affect the overall network properties and are at the same time network conformation and tension dependent.
Gene nodes with higher degrees turned out to be actually involved in important long genetic pathways, and for specific values of k, between 16 and 18, drastic changes may be observed in the network conformation, while emerging several clusters of genes.
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As previously found for the Internet and the World-Wide Web as well as for social and biological networks, the conformation space network is scale-free and contains highly connected hubs like the native state which is the most populated free energy basin.
Figure 6a, b presents side and top views, respectively, of distinct changes in the network chain conformation during the compression process.
Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression.
This network of alternative conformations (Arg-369, Glu-68, Cys-170, Leu-171, and a water) is not present in wild-type or V207A ADHs and does not appear to be an obligatory consequence of the V203A substitution because ∼60% of the subunits have residue interactions that are similar to those for the wild-type enzyme.
The conformation space network describes the significant free energy minima and their dynamic connectivity without requiring arbitrarily chosen reaction coordinates.
Vibrational investigations allowed us to obtain information on: (a) the network structure and the conformation of fluorocarbon hydrophobic domains of the Nafion host polymer, (b) the MxOy⋯HSO3R interactions occurring in ionic polar cages of membranes and (c) the various water domains present in the hydrophilic polar cages of membranes.
In fact the importance of the internal hydrogen bonding network in maintaining the conformation of the canonical loop has been demonstrated structurally across most families of standard mechanism inhibitors [50].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com